Bioinformatics books, courses, and other resources

Here are some books, courses, and software you may find helpful on your bioinformatics journey

Books to change your perspective

For building a great career

Cal Newport is a theoretical computer science professor, and his passion project for many years has been figuring of what makes people happy in their careers. He wrote a book called Deep Work: Rules for Focused Success in a Distracted World, that I found really resonated with me. The idea of deep work is something that I have applied a lot in my own work, and it really drove me to set better boundaries and protect some time every week and every day to actually get better at what I do, and not just put out email fires constantly.

I also highly recommend reading Cal Newport’s first book on this topic, So Good They Can’t Ignore You: Why Skills Trump Passion in the Quest for Work You Love which describes how getting really damn good at what you do gives you a better life than just trying to “find your passion.” This then becomes the reason to pursue Deep Work for yourself because it’s the best way to build those skills that will buy you the power of control over your working life.

I just zoomed through both these books in one weekend, and I find it easy to relate to Cal Newport when he talks about trying to succeed at graduate school and figuring out how to build a great career. This is a huge contrast to the way most people online talk about “finding your passion.” I find that I become passionate about something after getting really good at it and understanding it on a deeper level. This certainly happened with bioinformatics, and it even happened on a smaller scale with multiple school projects. I gave a presentation to my climate change class in college about electric cars back in 2010, so I liked Tesla before it was cool 😉 #hipster. I’ve been crazy about electric cars ever since that project. I vowed that my next car would be electric, so since I’m still poor (no Tesla money yet!), I now drive a cute little nerdy-looking Nissan Leaf. Anyway, you can build passion by learning and getting really good at things, and if you want to learn more about why deep work is more important than finding that elusive passion, go read Cal Newport’s books!

Bioinformatics Courses

These are some of the online courses I recommend you check out. Different people love and hate the same course, so feel free to skip around and just take a peak at what you find interesting. Bioinformatics is a huge field, so you don’t have to love all of its subfields, but this should give you a taste of a few different perspectives:

Genomic Data Science Specialization from Johns Hopkins on Coursera. Within that specialization I especially recommend Ben Langmead’s course using Python for working with DNA sequences. Ben is the creator of Bowtie who first figured out that the Burrows Wheeler Transform could be used to create an index of the genome for fast, efficient genome alignments, which made a big difference in the field.

For machine learning, Andrew Ng’s Machine Learning course on Coursera is a classic that I highly recommend.
I went through this and did all of the programming assignments in MatLab because I had just finished Linear Algebra. If you are not completely comfortable with linear algebra, skip the programming assignments and just watch the lectures.

Software

Sublime Text

A fantastic text editor that will color your code for multiple languages, run Python scripts, and let you manipulate data on multiple rows at once. It’s kind of magical.

ClipMenu

This neat little program (for Mac) is an upgrade for your clipboard, allowing you to copy multiple things and paste them again. This is such a time-saver and lets you remember that piece of code you copied but accidentally copied over it with something else, not you can just go down the list and find it again.

iTerm

iTerm is a replacement for the terminal on Mac. I switched to it after some frustration with creating multiple tabs and windows in the terminal, and I have never gone back (except to make the first bash tutorial video)

Recording setup:

1. Audio: Blue Raspberry Microphone

This sounds much clearer than my laptop’s or iPhone’s microphones.

2. Video: my iPhone 6

It turns out iPhones have pretty decent cameras. And I can plug the Blue Raspberry microphone straight into the iPhone.

3. Tripod from AmazonBasics

4. Screen recording: QuickTime Player (comes with Mac computers)

This works fantastically. There are paid screen recorders out there, but I haven’t had any problems just using QuickTime. It’s simple, high-quality, and makes circles whenever you click, so viewers can see what you are doing.

5. Video editing: iMovie (comes with Mac computers)

Pretty easy to use, tons of tutorials out there. I only ran into one oddity to look out for: If you want a high-resolution video, the very first footage or photo you add to a movie must have that high resolution. For some reason it sets the maximum resolution by the first piece of media you add, even if you remove it later, and there is no way to change it without starting over. Now I just have to be careful to check that the resolution is high right after adding the first media to the project.